@@ -127,7 +127,9 @@ importFrom(igraph,V)

 importFrom(igraph,add_edges)

 importFrom(igraph,as_adjacency_matrix)

 importFrom(igraph,as_incidence_matrix)

+importFrom(igraph,degree)

 importFrom(igraph,delete.edges)

+importFrom(igraph,delete_vertices)

 importFrom(igraph,get.edgelist)

 importFrom(igraph,graph.data.frame)

 importFrom(igraph,induced_subgraph)

@@ -29,8 +29,8 @@

 #' @importFrom graphics par plot

 #' @importFrom grDevices colorRampPalette rgb col2rgb

 #' @importFrom grid gpar

-#' @importFrom igraph add_edges as_adjacency_matrix as_incidence_matrix delete.edges

-#' "%du%" E "E<-" graph.data.frame induced_subgraph

+#' @importFrom igraph add_edges as_adjacency_matrix as_incidence_matrix degree

+#' delete.edges delete_vertices "%du%" E "E<-" graph.data.frame induced_subgraph

 #' make_full_graph permute.vertices strength V "V<-" vcount get.edgelist

 #' @importFrom matrixStats rowSds

 #' @importFrom methods is

@@ -16,6 +16,10 @@ ggs_backbone(

   bb_extract_alpha = 0.05,

   bb_extract_fwer = c("none", "bonferroni", "holm"),

   bb_fullinfo = FALSE,

+  bb_remove_singletons = TRUE,

+  color_graph = TRUE,

+  color_by_geneset = "z_score",

+  color_by_feature = "log2FoldChange",

   ...

 )

 }

@@ -59,6 +63,22 @@ either a simple \code{ìgraph} object with the graph backbone (if set to \code{F

 or a list object containing also the \code{backbone} object, and the gene-geneset

 graph used for the computation (if \code{TRUE})}

+\item{bb_remove_singletons}{Logical value, defines whether to remove or leave

+in the returned graph the nodes that are not connected to other vertices}

+

+\item{color_graph}{Logical value, specifies whether to use information about

+genesets or features to colorize the nodes, e.g. for this info to be used in

+interactive versions of the graph}

+

+\item{color_by_geneset}{Character string, corresponding to the column in

+\code{res_enrich} to be used for coloring the nodes if \code{bb_on} is set to "genesets".

+Defaults to the "z_score", which can be obtained via \code{get_aggrscores()}}

+

+\item{color_by_feature}{Character string, corresponding to the column in

+\code{res_de} to be used for coloring the nodes if \code{bb_on} is set to "features".

+Defaults to the "log2FoldChange", which should be normally included in a

+DESeqResults object.}

+

 \item{...}{Additional parameters to be passed internally}

 }

 \value{

@@ -106,16 +126,17 @@ data(res_enrich_macrophage, package = "GeneTonic")

 res_enrich <- shake_topGOtableResult(topgoDE_macrophage_IFNg_vs_naive)

 res_enrich <- get_aggrscores(res_enrich, res_de, anno_df)

-ggs <- ggs_graph(res_enrich,

-                 res_de,

-                 anno_df

-                )

-ggs_backbone <- ggs_backbone(res_enrich,

+ggs_bbg <- ggs_backbone(res_enrich,

                              res_de,

                              anno_df,

                              n_gs = 50,

-                             bb_on = "genesets"

+                             bb_on = "genesets",

+                             color_graph = TRUE,

+                             color_by_geneset = "z_score"

 )

-plot(ggs_backbone)

+plot(ggs_bbg)

+

+# if desired, one can also plot the interactive version

+visNetwork::visIgraph(ggs_bbg)

 }